HEADER VIRAL PROTEIN 21-JAN-20 6XV2 TITLE FULL STRUCTURE OF RYMV P1 PROTEIN, DERIVED FROM CRYSTALLOGRAPHIC AND TITLE 2 NMR DATA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: P1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICE YELLOW MOTTLE VIRUS; SOURCE 3 ORGANISM_TAXID: 31744; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PUTATIVE RNA BINDING PROTEIN; SILENCING SUPPRESSOR, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 14 AUTHOR V.POIGNAVENT,F.HOH,F.VIGNOLS,H.DEMENE,Y.YANG,F.X.GILLET REVDAT 3 14-JUN-23 6XV2 1 REMARK REVDAT 2 24-AUG-22 6XV2 1 JRNL REVDAT 1 03-FEB-21 6XV2 0 JRNL AUTH V.POIGNAVENT,F.HOH,G.TERRAL,Y.YANG,F.X.GILLET,J.H.KIM, JRNL AUTH 2 F.ALLEMAND,E.LACOMBE,C.BRUGIDOU,S.CIANFERANI,H.DEMENE, JRNL AUTH 3 F.VIGNOLS JRNL TITL A FLEXIBLE AND ORIGINAL ARCHITECTURE OF TWO UNRELATED ZINC JRNL TITL 2 FINGERS UNDERLIES THE ROLE OF THE MULTITASK P1 IN RYMV JRNL TITL 3 SPREAD. JRNL REF J.MOL.BIOL. V. 434 67715 2022 JRNL REFN ESSN 1089-8638 JRNL PMID 35798161 JRNL DOI 10.1016/J.JMB.2022.167715 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RIGID BODY REMARK 4 REMARK 4 6XV2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106342. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 220 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-99% 15N] RYMV P1, 100 REMARK 210 MM NONE NACL, 1 MM NONE DTT, 60 REMARK 210 MM NONE NA2SO4, 25 MM NONE TRIS, REMARK 210 90% H2O/10% D2O; 500 UM 15N RYMV REMARK 210 P1, 7 MG/ML NONE PF1 PHAGE, 200 REMARK 210 MM NONE NACL, 25 MM NONE TRIS, 1 REMARK 210 MM NONE DTT, 90% H2O/10% D2O; REMARK 210 200 UM [U-99% 13C; U-99% 15N] REMARK 210 RYMV P1, 100 MM NONE SODIUM REMARK 210 CHLORIDE, 25 MM NONE TRIS, 1 MM REMARK 210 NONE DTT, 60 MM NONE NA2SO4, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D HNCO; REMARK 210 3D HNCACB; 3D HCCH-TOCSY; 2D REMARK 210 TROSY; 2D HSQC IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, NMRVIEW, NMRPIPE, REMARK 210 GIFA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ALA A 139 93.03 -167.25 REMARK 500 2 ALA A 139 93.12 -167.14 REMARK 500 3 ALA A 139 93.10 -167.12 REMARK 500 4 ALA A 139 93.09 -167.10 REMARK 500 5 ALA A 139 92.99 -167.13 REMARK 500 6 ALA A 139 93.08 -167.20 REMARK 500 7 ALA A 139 93.11 -167.15 REMARK 500 8 ALA A 139 93.10 -167.23 REMARK 500 9 ALA A 139 93.14 -167.15 REMARK 500 10 ALA A 139 93.15 -167.09 REMARK 500 11 ALA A 139 93.09 -167.14 REMARK 500 12 ALA A 139 93.11 -167.08 REMARK 500 13 ALA A 139 93.08 -167.19 REMARK 500 14 ALA A 139 93.10 -167.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 64 SG REMARK 620 2 CYS A 67 SG 111.1 REMARK 620 3 CYS A 92 SG 109.7 112.8 REMARK 620 4 CYS A 95 SG 112.0 106.3 104.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 109 NE2 REMARK 620 2 CYS A 140 SG 109.3 REMARK 620 3 HIS A 145 ND1 108.5 104.1 REMARK 620 4 CYS A 149 SG 105.6 117.3 111.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6TY0 RELATED DB: PDB REMARK 900 RELATED ID: 6TY2 RELATED DB: PDB REMARK 900 RELATED ID: 27880 RELATED DB: BMRB DBREF 6XV2 A 1 157 UNP Q709H6 Q709H6_9VIRU 1 157 SEQRES 1 A 157 MET THR ARG LEU GLU VAL LEU ILE ARG PRO THR GLU GLN SEQRES 2 A 157 THR ALA ALA LYS ALA ASN ALA VAL GLY TYR THR HIS ALA SEQRES 3 A 157 LEU THR TRP VAL TRP HIS SER GLN THR TRP ASP VAL ASP SEQRES 4 A 157 SER VAL ARG ASP PRO SER LEU ARG ALA ASP PHE ASN PRO SEQRES 5 A 157 GLU LYS VAL GLY TRP VAL SER VAL SER PHE ALA CYS THR SEQRES 6 A 157 GLN CYS THR ALA HIS TYR TYR THR SER GLU GLN VAL LYS SEQRES 7 A 157 TYR PHE THR ASN ILE PRO PRO VAL HIS PHE ASP VAL VAL SEQRES 8 A 157 CYS ALA ASP CYS GLU ARG SER VAL GLN LEU ASP ASP GLU SEQRES 9 A 157 ILE ASP ARG GLU HIS GLN GLU ARG ASN ALA GLU ILE SER SEQRES 10 A 157 ALA CYS ASN ALA ARG ALA LEU SER GLU GLY ARG PRO ALA SEQRES 11 A 157 SER LEU VAL TYR LEU SER ARG ASP ALA CYS ASP ILE PRO SEQRES 12 A 157 GLU HIS SER GLY ARG CYS ARG PHE VAL LYS TYR LEU ASN SEQRES 13 A 157 PHE HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 THR A 14 VAL A 21 1 8 HELIX 2 AA2 SER A 33 ASP A 37 5 5 HELIX 3 AA3 ASP A 94 GLU A 126 1 33 HELIX 4 AA4 ILE A 142 SER A 146 5 5 SHEET 1 AA1 4 ALA A 26 HIS A 32 0 SHEET 2 AA1 4 THR A 2 PRO A 10 -1 N LEU A 4 O VAL A 30 SHEET 3 AA1 4 SER A 45 CYS A 64 1 O LEU A 46 N LEU A 7 SHEET 4 AA1 4 HIS A 70 THR A 81 -1 O TYR A 71 N PHE A 62 SHEET 1 AA2 4 ALA A 26 HIS A 32 0 SHEET 2 AA2 4 THR A 2 PRO A 10 -1 N LEU A 4 O VAL A 30 SHEET 3 AA2 4 SER A 45 CYS A 64 1 O LEU A 46 N LEU A 7 SHEET 4 AA2 4 VAL A 86 VAL A 90 1 O PHE A 88 N SER A 61 LINK SG CYS A 64 ZN ZN A 201 1555 1555 2.18 LINK SG CYS A 67 ZN ZN A 201 1555 1555 2.18 LINK SG CYS A 92 ZN ZN A 201 1555 1555 2.35 LINK SG CYS A 95 ZN ZN A 201 1555 1555 2.44 LINK NE2 HIS A 109 ZN ZN A 202 1555 1555 2.07 LINK SG CYS A 140 ZN ZN A 202 1555 1555 2.35 LINK ND1 HIS A 145 ZN ZN A 202 1555 1555 1.98 LINK SG CYS A 149 ZN ZN A 202 1555 1555 2.29 SITE 1 AC1 4 CYS A 64 CYS A 67 CYS A 92 CYS A 95 SITE 1 AC2 4 HIS A 109 CYS A 140 HIS A 145 CYS A 149 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1